Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,276,099 T→A 8.5% T146T (ACT→ACA)  tsf → Elongation factor Ts

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,276,0990TA 8.5% 145.4 / 7.0 47T146T (ACT→ACA) tsfElongation factor Ts
Reads supporting (aligned to +/- strand):  ref base T (18/25);  new base A (2/2);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.19e-01

GTATTAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCAACCCTAAATATGT  >  USA300TCH1516_ALE/1275959‑1276239
                                                                                                                                            |                                                                                                                                            
gTATTAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACt                                                                                                                                              <  1:313904/141‑1 (MQ=255)
gTATTAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACt                                                                                                                                              <  1:21865/141‑1 (MQ=255)
gTATTAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACt                                                                                                                                              <  1:204310/141‑1 (MQ=255)
    tAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTaaaa                                                                                                                                          >  2:167999/1‑141 (MQ=255)
     aGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAAc                                                                                                                                         >  2:352047/1‑141 (MQ=255)
             aaGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACg                                                                                                                                 >  2:195587/1‑141 (MQ=255)
                   aaaCTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGGAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCtt                                                                                                                           <  1:234182/141‑1 (MQ=255)
                   aaaCTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCtt                                                                                                                           >  2:434571/1‑141 (MQ=255)
                   aaaCTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCtt                                                                                                                           >  2:380683/1‑141 (MQ=255)
                   aaaCTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCtt                                                                                                                           <  1:421196/141‑1 (MQ=255)
                   aaaCTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCtt                                                                                                                           <  2:192925/141‑1 (MQ=255)
                   aaaCTGTTGAAGCTATAATGGGAACAACTGTACCACATGGTAAATCAGGTGATGAAAGAATTAAAGAAGCAATTTCAACACTCGGTGAAAAAGTAAGTGATCGTCGTGTTGCTATCGGAACTAACACTGATAACGAAGCtt                                                                                                                           >  2:419275/1‑141 (MQ=255)
                       tGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCgg                                                                                                                       <  1:196627/141‑1 (MQ=255)
                           gAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGct                                                                                                                   <  1:143887/141‑1 (MQ=255)
                                    aTGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTacac                                                                                                          >  2:276695/1‑141 (MQ=255)
                                           caacTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTg                                                                                                   <  2:7662/141‑1 (MQ=255)
                                           caacTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTg                                                                                                   <  2:152500/141‑1 (MQ=255)
                                           caacTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTg                                                                                                   >  1:177188/1‑141 (MQ=255)
                                             acTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACAAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGa                                                                                                 >  1:302240/1‑141 (MQ=255)
                                             acTTTACCAAATGGTAAATAAGAAGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACAAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGa                                                                                                 >  1:378295/1‑141 (MQ=255)
                                              cTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGAc                                                                                                <  1:171993/141‑1 (MQ=255)
                                              cTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGAc                                                                                                >  2:283291/1‑141 (MQ=255)
                                                      aaTGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGgt                                                                                        <  1:369003/141‑1 (MQ=255)
                                                       aTGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGgtg                                                                                       <  2:260953/141‑1 (MQ=255)
                                                       aTGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGgtg                                                                                       <  1:69417/141‑1 (MQ=255)
                                                        tGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGgtgt                                                                                      <  2:164693/141‑1 (MQ=255)
                                                        tGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGgtgt                                                                                      <  2:431209/141‑1 (MQ=255)
                                                            aaaTCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTa                                                                                  >  1:377313/1‑141 (MQ=255)
                                                            aaaTCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTa                                                                                  >  2:218044/1‑141 (MQ=255)
                                                                                tAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAAc                                                              <  2:9050/141‑1 (MQ=255)
                                                                                 aaaGAAGCAATTTCAACAATCGGTGAAAAAGTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAAATTATAATGACGCTTTCGGCGCTGACTTACACATGGGTGGAGGCAGTGGGGTATTAACAGGTGTTGAAGGTTCAACt                                                             >  1:114875/1‑141 (MQ=255)
                                                                                     aagCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACg                                                         >  1:80115/1‑141 (MQ=255)
                                                                                                 caaTCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACAAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCaa                                             <  2:378295/141‑1 (MQ=255)
                                                                                                 caaTCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACAAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCaa                                             <  2:302240/141‑1 (MQ=255)
                                                                                                   aTCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAaga                                           <  2:257541/141‑1 (MQ=255)
                                                                                                   aTCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAaga                                           >  2:107318/1‑141 (MQ=255)
                                                                                                     cGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAgaga                                         <  1:167999/141‑1 (MQ=255)
                                                                                                       gTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACg                                       <  1:421922/141‑1 (MQ=255)
                                                                                                       gTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACg                                       <  2:434878/141‑1 (MQ=255)
                                                                                                       gTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACg                                       <  2:443119/141‑1 (MQ=255)
                                                                                                                tAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGc                              <  1:352047/141‑1 (MQ=255)
                                                                                                                   gtgtTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCata                           <  2:177188/141‑1 (MQ=255)
                                                                                                                        cgtcgtTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCt                      <  2:424940/141‑1 (MQ=255)
                                                                                                                        cgtcgtTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCt                      <  2:251413/141‑1 (MQ=255)
                                                                                                                          tcgtTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGc                    >  1:345839/1‑141 (MQ=255)
                                                                                                                          tcgtTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGc                    >  2:63418/1‑141 (MQ=255)
                                                                                                                             ttttGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAAt                 <  2:377313/141‑1 (MQ=255)
                                                                                                                               ttGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTGGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCa               <  1:276695/141‑1 (MQ=255)
                                                                                                                                    aTCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCAACCCt          >  2:458659/1‑141 (MQ=255)
                                                                                                                                          aCTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCAACCCTAAatat    >  2:347016/1‑141 (MQ=255)
                                                                                                                                            tAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCAACCCTAAATATGt  <  2:222597/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
GTATTAGATACAAAAGCTGAAACTGTTGAAGCTTTAATGGAAACAACTTTACCAAATGGTAAATCAGTTGATGAAAGAATTAAAGAAGCAATTTCAACAATCGGTGAAAAATTAAGTGTTCGTCGTTTTGCTATCAGAACTAAAACTGATAACGATGCTTTCGGCGCTTACTTACACATGGGTGGACGCATTGGTGTATTAACAGTTGTTGAAGGTTCAACTGACGAAGAAGCAGCAAGAGACGTTGCTATGCATATCGCTGCAATCAACCCTAAATATGT  >  USA300TCH1516_ALE/1275959‑1276239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑